US10113193B2 - Method for optimizing the assembly and production of hetero-multimeric protein complexes - Google Patents

Method for optimizing the assembly and production of hetero-multimeric protein complexes Download PDF

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US10113193B2
US10113193B2 US15/086,736 US201615086736A US10113193B2 US 10113193 B2 US10113193 B2 US 10113193B2 US 201615086736 A US201615086736 A US 201615086736A US 10113193 B2 US10113193 B2 US 10113193B2
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Giovanni Magistrelli
Pauline Malinge
Yves Poitevin
Nicolas Fischer
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Novimmune SA
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    • C12P21/00—Preparation of peptides or proteins
    • C12P21/005—Glycopeptides, glycoproteins
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
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    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/46—Hybrid immunoglobulins
    • C07K16/468—Immunoglobulins having two or more different antigen binding sites, e.g. multifunctional antibodies
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/67—General methods for enhancing the expression
    • C—CHEMISTRY; METALLURGY
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    • C12P21/00—Preparation of peptides or proteins
    • C12P21/02—Preparation of peptides or proteins having a known sequence of two or more amino acids, e.g. glutathione
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
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    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
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    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance
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    • C12N2800/00—Nucleic acids vectors
    • C12N2800/22—Vectors comprising a coding region that has been codon optimised for expression in a respective host

Definitions

  • Methods are provided to improve the expression of protein complexes by tuning the expression levels of each component required for the assembly of the complex. These methods are effective in limiting the expression of the dominant chain and, thus, equilibrating their relative abundance.
  • the methods provided herein lead to a significant increase in productivity and final bispecific yields both in transient expression systems as well as in stably transfected mammalian cells.
  • Recombinant expression in bacterial, yeast, insect, plant or mammalian cells is fundamental for the production of proteins that are used for research as well as therapeutic applications.
  • the yield of recombinant protein expression in Chinese Hamster Ovary (CHO) cells has been significantly enhanced by optimizing multiple parameters such as culture medium composition, fermentation parameters, as well as optimization of the constructs that are used to drive the expression of the gene encoding the recombinant protein of interest.
  • Some proteins are composed of several polypeptides that can associate in complexes that can be covalently or non-covalently linked.
  • Antibodies are an example of such a class of proteins as they are composed of four polypeptides (i.e. two heavy chains and two light chains) that are linked by disulfide bonds. Due to their commercial and therapeutic importance, the expression of antibodies in CHO cells has been the subject of intense efforts of optimization, aiming at maximizing the expression of the two chains that compose the antibody. However, major differences can be observed as the levels of expression can vary up to 200-fold between antibodies.
  • the methods of the disclosure improve the expression of protein complexes by tuning the expression levels of each component required for the assembly of the complex.
  • reducing the expression of one or several polypeptides in the protein complex enhances the assembly and yield of the protein complex.
  • the method is particularly suited to optimize the expression and yield of bispecific antibodies that often rely on the co-expression of multiple polypeptides.
  • the unbalanced expression (too high or too low) of one of the components can lead to a significant decrease of the desired final product and an increase in the production of unwanted side-products. This limitation can impact both IgG-like bispecific formats as well as formats based on antibody fragments.
  • the method is in particular applicable for the optimization of the expression of bispecific antibodies named KA-bodies (Fischer et al., Exploiting light chains for the scalable generation and platform purification of native human bispecific IgG. Nat. Comms, 6: 6113 (2015)).
  • This technology produces a fully-human bispecific antibody (BsAb), composed of a common heavy chain and two different light chains (one kappa and one lambda) (see e.g., WO 2012/023053).
  • a proprietary tricistronic vector including these three chains is introduced in mammalian cells to produce the bispecific antibodies ( ⁇ -bodies) that contain one ⁇ and one ⁇ chains in addition to the two monospecific antibodies IgG ⁇ and IgG ⁇ .
  • the ratio for the three molecules should be 25% IgG ⁇ , 25% IgG ⁇ , and 50% IgG ⁇ .
  • an unbalanced expression level of the two chains is sometimes observed, leading a decrease in bispecific yield.
  • One solution could be to increase the expression of the less expressed chain to restore the balance.
  • this approach has been unsuccessful (as shown in the working examples provided herein).
  • the methods of the disclosure are effective in limiting the expression of the dominant chain and, thus, equilibrating their relative abundance.
  • the methods disclosed herein lead to a significant increase in productivity and final bispecific yields both in transient expression systems as well as in stably transfected CHO cells.
  • the reduction of the expression of one or several polypeptides can lead to an overall increase in productivity.
  • the examples provided herein use ⁇ -bodies, the methods disclosed herein are applicable to other bispecific antibody formats and any other protein complex composed of several different polypeptides.
  • the disclosure provides methods to increase the production yield of a protein complex composed of several polypeptides by decreasing the expression rate of one or several of the polypeptides.
  • the reduction in expression of one of the polypeptides is achieved by modification of transcription rate, translation rate, or mRNA stability.
  • the reduction in expression rate of one of the polypeptides is achieved by the modifying the mRNA secondary structure.
  • the reduction in expression of one of the polypeptides is achieved by modifying transcription rate, modifying translation rate, modifying mRNA stability, modifying mRNA secondary structure or by a combination of any of these factors.
  • the reduction in expression of one of the polypeptides in the protein complex is achieved by modifying translation rate. In some embodiments, the reduction in expression of one of the polypeptides in the protein complex is achieved by altering the codon composition of that polypeptide. In some embodiments, the reduction in expression of one of the polypeptides in the protein complex is achieved by modifying translation rate and altering the codon composition of that polypeptide.
  • the reduction in expression of one of the polypeptides in the protein complex is achieved by modifying translation rate. In some embodiments, the reduction in expression of one of the polypeptides in the protein complex is achieved by altering the codon composition of that polypeptide via the replacement of certain codons with codons that are less frequently used in the host cell that is used for expression of the protein complex. In some embodiments, the reduction in expression of one of the polypeptides in the protein complex is achieved by modifying translation rate, and altering the codon composition of that polypeptide via the replacement of certain codons with codons that are less frequently used in the host cell that is used for expression of the protein complex.
  • the reduction in expression of one of the polypeptides in the protein complex is achieved by modifying translation rate. In some embodiments, the reduction in expression of one of the polypeptides in the protein complex is achieved by altering the codon composition of that polypeptide via the replacement of certain codons with codons that are less frequently used in a mammalian host cell used for expression of the protein complex. In some embodiments, the reduction in expression of one of the polypeptides in the protein complex is achieved by modifying translation rate and altering the codon composition of that polypeptide via the replacement of certain codons with codons that are less frequently used in a mammalian host cell used for expression of the protein complex.
  • the protein complex is a multispecific antibody. In some embodiments, the protein complex is a bispecific antibody. In some embodiments, the bispecific antibody is a composed of two different light chains and a common heavy chain.
  • the bispecific antibody includes a human lambda light chain and a human kappa light chain.
  • the bispecific antibody includes a first and the second antigen-binding regions each comprise at least one complementarity determining region (CDR).
  • the first and the second antigen-binding regions each comprise at least two CDRs.
  • the first and the second antigen-binding regions each comprise each comprise three CDRs.
  • the CDRs are from an immunoglobulin heavy chain.
  • the heavy chain is a human heavy chain.
  • the CDRs are from a lambda light chain.
  • the CDRs are from a kappa light chain.
  • the first antigen-binding region comprises a first immunoglobulin heavy chain variable domain
  • the second antigen-binding region comprises a second immunoglobulin heavy chain variable domain
  • the first and the second immunoglobulin heavy chain variable domains independently comprise a human CDR, a mouse CDR, a rat CDR, a rabbit CDR, a monkey CDR, an ape CDR, a synthetic CDR, and/or a humanized CDR.
  • the CDR is human and is somatically mutated.
  • the bispecific antibodies comprise a human framework region (FR).
  • the human FR is a somatically mutated human FR.
  • the bispecific antibodies are obtained by screening a phage library comprising antibody variable regions for reactivity toward an antigen of interest.
  • the first and/or the second antigen-binding regions of the bispecific antibodies are obtained by immunizing a non-human animal such as a mouse, a rat, a rabbit, a monkey, or an ape with an antigen of interest and identifying an antibody variable region nucleic acid sequence encoding variable region specific for the antigen of interest.
  • the bispecific antibody is a fully human bispecific antibody and has an affinity for each epitope, independently, in the micromolar, nanomolar, or picomolar range.
  • the bispecific antibody is non-immunogenic or substantially non-immunogenic in a human. In some embodiments, the bispecific antibody lacks a non-native human T-cell epitope. In some embodiments, the modification of the CHl region is non-immunogenic or substantially non-immunogenic in a human.
  • the antigen-binding protein comprises a heavy chain, wherein the heavy chain is non-immunogenic or substantially non-immunogenic in a human.
  • the heavy chain has an amino acid sequence that does not contain a non-native T-cell epitope. In some embodiments, the heavy chain comprises an amino acid sequence whose proteolysis cannot form an amino acid sequence of about 9 amino acids that is immunogenic in a human. In a specific embodiment, the human is a human being treated with the antigen-binding protein. In some embodiments, the heavy chain comprises an amino acid sequence whose proteolysis cannot form an amino acid sequence of about 13 to about 17 amino acids that is immunogenic in a human. In a specific embodiment, the human is a human being treated with the antigen-binding protein.
  • more than one protein complex is co-expressed. In some embodiments, more than one antibody is co-expressed.
  • FIG. 1 is an illustration depicting the mutations introduced in the lambda light chain to modulate its expression.
  • the polynucleotide sequences (from top to bottom) correspond to SEQ ID NOs: 5-9, respectively, as shown in Table 1.3.
  • FIG. 2 is a graph indicating the concentration of IgG1 antibodies obtained in the supernatant of producing Peak cells measured using the OCTET technology.
  • FIG. 3A is a graph of HIC profile of total purified IgG.
  • FIG. 3B is a graph showing the different percentage of monospecific kappa antibody, monospecific lambda antibody, and bispecific IgG for the different constructs and that were derived from the RIC profiles.
  • FIG. 4 is an isoelectric focusing polyacrylamide gel showing the expression of monoclonal and bispecific antibodies after affinity purification with CaptureSelect IgG Fc XL resin.
  • FIG. 5 is a series of graphs indicating the total IgG productivity for different constructs from several CHO cells pools.
  • FIG. 6A is gel-like image representation of an Agilent protein 80 chip run monitoring the sizes of the heavy and light chains from purified IgG in reducing and denaturing conditions.
  • FIG. 6B is a graph showing the ratio of total kappa and lambda light chains for several CHO pools for each construct.
  • FIG. 7 is a series of graphs showing the distribution in % for mono Kappa, mono Lambda and bispecific antibodies expressed by several CHO cell pools.
  • FIG. 8 is a graph depicting the results of an ELISA showing the specific binding of each arm of the bispecific antibody against two targets (hCD19 and hCD47) as well as an irrelevant control protein (hIL6R).
  • Recombinant expression in bacterial, yeast, insect, plant or mammalian cells is fundamental for the production of proteins that are used for research as well as therapeutic applications.
  • the yield of recombinant protein expression in Chinese Hamster Ovary cells has been significantly enhanced by optimizing multiple parameters such as culture medium composition, fermentation parameters, as well as optimization of the constructs that are used to drive the expression of the gene encoding the recombinant protein of interest.
  • These include the improvements at transcriptional and translational levels as well as mRNA secondary structures and stability.
  • Another important element is the optimization of codon usages so that it matches the expression host and avoid limitation due to low abundance tRNAs.
  • the optimization process also can also include the removal of sequence repeats, killer motifs and splice sites and stable RNA secondary structures are avoided.
  • the codon usage and GC content can be simultaneously adapted for the expression in CHO cells or other host cells. The aim of such modifications is to maximize translation and stability of RNA so that translation and thus expression of the desired polypeptide is maximal.
  • Some proteins are composed of several polypeptides that can associate in complexes that can be covalently or non-covalently linked.
  • Antibodies are an example of such a class of proteins as they are composed of four polypeptides (i.e. two heavy chains and two light chains) that are linked by disulfide bonds.
  • Antibodies carry a unique specificity for a target antigen that is driven by the Fab portion while they can engage with the immune via their Fc portion.
  • a number of currently used biological therapeutics for cancer are monoclonal antibodies directed against antigens that are over expressed by targeted cancer cells.
  • ADCC antibody-dependent cellular toxicity
  • CDC complement-dependent cytotoxicity
  • bispecific antibodies capable of engaging more than one antigen, e.g., bispecific antibodies.
  • a large number of bispecific antibody formats have been described and two bispecific antibodies have been approved so far while many others are currently in clinical trials (Kontermann R E, Brinkmann U., Bispecific antibodies, Drug Discover Today, (2015), available at dx.doi.org/10.1016/j.drudis.2015.02.2008).
  • the bispecific antibody is composed of more than two polypeptides.
  • the correct assembly can be based on random pairing of the chains, leading to a mixture of molecules from which the bispecific antibody can be purified.
  • the interface of the chains can be engineered so that the desired pairing can be preferably obtained.
  • the co-expression of multiple chains implies a higher complexity and the relative expression rates and thus abundance of the chains composing the bispecific molecule can potentially have a major impact on overall yield and efficiency in assembly.
  • the methods of the disclosure improve the expression of protein complexes by tuning the expression levels of each component required for the assembly of the complex.
  • the methods of the disclosure are effective in limiting the expression of the dominant chain and, thus, equilibrating their relative abundance.
  • the methods disclosed herein lead to a significant increase in productivity and final bispecific yields both in transient expression systems as well as in stably transfected CHO cells.
  • the reduction of the expression of one or several polypeptides can lead to an overall increase in productivity.
  • Table 1 is a table depicting the constructs generated with different sequence optimization and deoptimization levels.
  • VHCH WT (SEQ ID NO: 1) and VHCH OPT (SEQ ID NO: 2) sequences VHCH 1 ATGGAATGGAGCTGGGTCTTTCTCTTCTTCCTGTCAGTAACTACAGGTGT VHCH OPT 1 ATGGAATGGTCCTGGGTGTTCCTGTTCTTCCTGTCCGTGACCACCGGCGT VHCH 51 CCACTCCGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTG VHCH OPT 51 CCACTCCGAGGTGCAGCTGCTGGAATCTGGCGGCGGACTGGTCCAGCCTG VHCH 101 GGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGC VHCH OPT 101 GAGGCTCCCTGAGACTGTCTTGCGCCGCCTCCGGCTTCACCTTCTCCAGC VHCH 151 TATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGT VHCH OPT 151 TATGCCATGAGCTGGG
  • VKCK WT (SEQ ID NO: 3) and VKCK OPT (SEQ ID NO: 4) sequences VKCK 1 ATGAGTGTGCCCACTCAGGTCCTGGGGTTGCTGCT GCTGTGGCTTACAGATGCCAGATGTGACATCCAGA VKCK 1 ATGTCCGTGCCCACCCAGGTGCTGGGACTGCTGCT OPT GCTGTGGCTGACCGACGCCAGATGCGACATCCAGA VKCK 71 TGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTA GGAGACAGAGTCACCATCACTTGCCAGGCGAGTCA VKCK 71 TGACCCAGAGCCCTTCCAGCCTGAGCGCCTCCGTG OPT GGCGACAGAGTGACCATCACCTGTCAGGCCTCCCA VKCK 141 GTCCATTAGTAGTTATTTAAATTGGTATCAGCAGA AACCAGGGAAAGCCCCTAAGCTCCTGATCTACGCT VKCK 141 GTCCATCTCCTCCTACCTGAACTGGTA
  • VLCL2DEOPT_1 TGGAAGAGTCATCGAAGCTACTCATGCCAAGTGACCCACGAGGGATCTACAGTCGAGA AAACCGTGGCTCCAACTGAGTGTTCCTAA VLCL2DEOPT_2 631 TGGAAATCACACCGTAGCTACTCATGCCAAGTAACCCACGAAGGGTCAACCGTAGAAA AAACTGTAGCACCGACCGAGTGCAGCTAA VLCL2DEOPT_3 631 TGGAAATCGCATCGTTCGTATTCGTGCCAAGTAACGCATGAAGGGTCGACGGTAGAAA AAACGGTAGCGCCGACGGAATGTTCGTAA Sequences for VLCL2 WT (SEQ ID NO: 5, shown in row 1 of the alignment), VLCL2 OPT (SEQ ID NO: 6, shown in row 2 of the alignment), VLCL2 OPT (SEQ ID NO: 6, shown in row 2 of the alignment), VLCL2 OPT (SEQ ID NO: 6, shown in row 2 of the alignment), VLCL2
  • Table 2 is a table showing the following data for each construct: total IgG and bispecific antibody quantity after purification as well as the proportion of bispecific determined by HIC.
  • Table 3 depicts total IgG productivity, bispecific % by HIC after protein A purification, and the amount of purified bispecific from CHO cell culture supernatant for representative pools for each construct.
  • polynucleotides and constructs thereof used in the methods provided herein can be generated synthetically by a number of different protocols known to those of skill in the art.
  • Appropriate polynucleotide constructs are purified using standard recombinant DNA techniques as described in, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, 2 nd Ed , (1989) Cold Spring Harbor Press, Cold Spring Harbor, N.Y., and under current regulations described in United States Dept. of HHS, National Institute of Health (NIH) Guidelines for Recombinant DNA Research.
  • a single vector e.g., a plasmid
  • a single vector will contain nucleic acid coding sequence for a single peptide display scaffold.
  • a single vector e.g., a plasmid
  • Viral and non-viral vectors may be prepared and used, including plasmids, which provide for replication of biosensor-encoding DNA and/or expression in a host cell.
  • the choice of vector will depend on the type of cell in which propagation is desired and the purpose of propagation. Certain vectors are useful for amplifying and making large amounts of the desired DNA sequence. Other vectors are suitable for expression in cells in culture. Still other vectors are suitable for transformation and expression in cells in a whole animal or person. The choice of appropriate vector is well within the skill of the art. Many such vectors are available commercially.
  • To prepare the constructs the partial or full-length polynucleotide is inserted into a vector typically by means of DNA ligase attachment to a cleaved restriction enzyme site in the vector.
  • the desired nucleotide sequence can be inserted by homologous recombination in vivo. Typically this is accomplished by attaching regions of homology to the vector on the flanks of the desired nucleotide sequence. Regions of homology are added by ligation of oligonucleotides, or by polymerase chain reaction using primers comprising both the region of homology and a portion of the desired nucleotide sequence, for example.
  • expression cassettes or systems that find use in, among other applications, the synthesis of the peptide display scaffolds.
  • the gene product encoded by a polynucleotide of the disclosure is expressed in any convenient expression system, including, for example, bacterial, yeast, insect, amphibian and mammalian systems. Suitable vectors and host cells are described in U.S. Pat. No. 5,654,173.
  • a polynucleotide is linked to a regulatory sequence as appropriate to obtain the desired expression properties.
  • These regulatory sequences can include promoters (attached either at the 5′ end of the sense strand or at the 3′ end of the antisense strand), enhancers, terminators, operators, repressors, and inducers.
  • the promoters can be regulated or constitutive. In some situations it may be desirable to use conditionally active promoters, such as tissue-specific or developmental stage-specific promoters. These are linked to the desired nucleotide sequence using the techniques described above for linkage to vectors. Any techniques known in the art can be used. In other words, the expression vector will provide a transcriptional and translational initiation region, which may be inducible or constitutive, where the coding region is operably linked under the transcriptional control of the transcriptional initiation region, and a transcriptional and translational termination region. These control regions may be native to the species from which the nucleic acid is obtained, or may be derived from exogenous sources.
  • Eukaryotic promoters suitable for use include, but are not limited to, the following: the promoter of the mouse metallothionein I gene sequence (Hamer et al., J. Mol. Appl. Gen. 1:273-288, 1982); the TK promoter of Herpes virus (McKnight, Cell 31:355-365, 1982); the SV40 early promoter (Benoist et al., Nature (London) 290:304-310, 1981); the yeast gall gene sequence promoter (Johnston et al., Proc. Natl. Acad., Sci. (USA) 79:6971-6975, 1982); Silver et al., Proc. Natl. Acad. Sci. (USA) 81:5951-59SS, 1984), the CMV promoter, the EF-1 promoter, Ecdysone-responsive promoter(s), tetracycline-responsive promoter, and the like.
  • Promoters may be, furthermore, either constitutive or regulatable.
  • Inducible elements are DNA sequence elements that act in conjunction with promoters and may bind either repressors e.g., lacO/LAC Iq repressor system in E. coli ) or inducers (e.g., gall/GAL4 inducer system in yeast). In such cases, transcription is virtually “shut off” until the promoter is derepressed or induced, at which point transcription is “turned-on.”
  • Expression vectors generally have convenient restriction sites located near the promoter sequence to provide for the insertion of nucleic acid sequences encoding heterologous proteins.
  • a selectable marker operative in the expression host may be present.
  • Expression vectors may be used for, among other things, the screening methods described in greater detail below.
  • Expression cassettes may be prepared comprising a transcription initiation region, the gene or fragment thereof, and a transcriptional termination region. After introduction of the DNA, the cells containing the construct may be selected by means of a selectable marker the cells expanded and then used for expression.
  • a unicellular organism such as E. coli, B. subtilis, S. cerevisiae , insect cells in combination with baculovirus vectors, or cells of a higher organism such as vertebrates, e.g., COS 7 cells, HEK 293, CHO, Xenopus Oocytes, etc.
  • vertebrates e.g., COS 7 cells, HEK 293, CHO, Xenopus Oocytes, etc.
  • Specific expression systems of interest include bacterial, yeast, insect cell and mammalian cell derived expression systems.
  • Expression systems in bacteria include those described in Chang et al., Nature (1978) 275:615; Goeddel et al., Nature (1979) 281:544; Goeddel et al., Nucleic Acids Res . (1980) 8:4057; EP 0 036,776; U.S. Pat. No. 4,551,433; DeBoer et al., Proc. Natl. Acad. Sci . ( USA ) (1983) 80:21-25; and Siebenlist et al., Cell (1980) 20:269.
  • Mammalian expression is accomplished as described in Dijkema et al., EMBO J . (1985) 4:761, Gorman et al., Proc. Natl. Acad. Sci . ( USA ) (198) 79:6777, Boshart et al., Cell (1985) 41:521 and U.S. Pat. No. 4,399,216.
  • Other features of mammalian expression are facilitated as described in Ham and Wallace, Meth. Enz . (1979) 58:44, Barnes and Sato, Anal. Biochem . (1980) 102:255, U.S. Pat. Nos. 4,767,704, 4,657,866, 4,927,762, 4,560,655, WO 90/103430, WO 87/00195, and U.S. RE 30,985.
  • the type of host cells suitable for use can vary widely.
  • the cell is a bacterial cell, a yeast cell or a mammalian cell.
  • the biological entity is a bacterial cell.
  • the bacterial cell is Escherichia coli, Shigella sonnei, Shigella dysenteriae, Shigella flexneri, Salmonella typhii, Salmonella typhimurium, Salmonella enterica, Enterobacter aerogenes, Serratia marcescens, Yersinia pestis, Bacillus cereus, Bacillus subtilis , or Klebsiella pneumoniae.
  • the constructs can be introduced into the host cell by any one of the standard means practiced by one with skill in the art to produce a cell line of the disclosure.
  • the nucleic acid constructs can be delivered, for example, with cationic lipids (Goddard, et al, Gene Therapy, 4:1231-1236, 1997; Gorman, et al, Gene Therapy 4:983-992, 1997; Chadwick, et al, Gene Therapy 4:937-942, 1997; Gokhale, et al, Gene Therapy 4:1289-1299, 1997; Gao, and Huang, Gene Therapy 2:710-722, 1995, all of which are incorporated by reference herein), using viral vectors (Monahan, et al, Gene Therapy 4:40-49, 1997; Onodera, et al, Blood 91:30-36, 1998, all of which are incorporated by reference herein), by uptake of “naked DNA”, and the like.
  • polynucleotide as referred to herein means a polymeric boron of nucleotides of at least 10 bases in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide.
  • the term includes single and double stranded forms of DNA.
  • polypeptide is used herein as a generic term to refer to native protein, fragments, or mutants of a polypeptide sequence. Hence, native protein fragments, and mutants are species of the polypeptide genus.
  • Preferred polypeptides in accordance with the disclosure comprise cytokines and antibodies.
  • antibody refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen.
  • Ig immunoglobulin
  • Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, F ab , F ab′ and F (ab′)2 fragments, and antibodies in an F ab expression library.
  • bind or “immunoreacts with” is meant that the antibody reacts with one or more antigenic determinants of the desired antigen and does not react (i.e., bind) with other polypeptides or binds at much lower affinity (K d >10 ⁇ 6 ) with other polypeptides.
  • the basic antibody structural unit is known to comprise a tetramer.
  • Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa).
  • the amino-terminal portion of each chain includes a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition.
  • the carboxy-terminal portion of each chain defines a constant region primarily responsible for effector function.
  • Human light chains are classified as kappa and lambda light chains.
  • Heavy chains are classified as mu, delta, gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively.
  • the variable and constant regions are joined by a “J” region of about 12 or more amino acids, with the heavy chain also including a “D” region of about 10 more amino acids. See generally, Fundamental immunology Ch. 7 (Paul, W., ea., 2nd ed. Raven Press, N.Y. (1989)).
  • the variable regions of each light/heavy chain pair form the antibody binding site.
  • MAb monoclonal antibody
  • CDRs complementarity determining regions
  • antibody molecules obtained from humans relate to any of the classes IgG, IgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain present in the molecule, Certain classes have subclasses as well, such as IgG 1 , IgG 2 , and others.
  • the light chain may be a kappa chain or a lambda chain.
  • fragments thereof shall mean a segment of a polynucleotide sequence or polypeptide sequence that is less than the length of the entire sequence. Fragments as used herein comprised functional and non-functional regions. Fragments from different polynucleotide or polypeptide sequences are exchanged or combined to create a hybrid or “chimeric” molecule. Fragments are also used to modulate polypeptide binding characteristics to either polynucleotide sequences or to other polypeptides.
  • promoter sequence shall mean a polynucleotide sequence comprising a region of a gene at which initiation and rate of transcription are controlled.
  • a promoter sequence comprises an RNA polymerase binding site as well as binding sites for other positive and negative regulatory elements. Positive regulatory elements promote the expression of the gene under control of the promoter sequence. Negative regulatory elements repress the express of the gene under control of the promoter sequence.
  • Promoter sequences used herein are found either upstream or internal to the gene being regulated. Specifically, the term “first promoter sequence” versus “second promoter sequence” refers to the relative position of the promoter sequence within the expression vector. The first promoter sequence is upstream of the second promoter sequence.
  • selection gene shall mean a polynucleotide sequence encoding for a polypeptide that is necessary for the survival of the cell in the given culture conditions. If a cell has successfully incorporated the expression vector carrying the gene of interest, along with the selection gene, that cell will produce an element that will allow it to selectively survive under hostile culture conditions. “Selected” cells are those which survive under selective pressure and must have incorporated the expression vector. The term “selective pressure” as used herein shall mean the addition of an element to cell culture medium that inhibits the survival of cells not receiving the DNA composition.
  • exogenous gene shall mean a gene encompassed within the genomic sequence of a cell.
  • exogenous gene shall mean a gene not encompassed within the genomic sequence of a cell. Exogenous genes are introduced into cells by the instant methods.
  • transgene as used herein shall mean a gene that has been transferred from one organism to another.
  • Examples of unconventional amino acids include: 4 hydroxyproline, ⁇ -carboxyglutamate, ⁇ -N,N,N-trimethyllysine, ⁇ -N-acetyllysine, O-phosphoserine, N-acetylserine, N-formylmethionine, 3-methylhistidine, 5-hydroxylysine, ⁇ -N-methylarginine, and other similar amino acids and imino acids e.g., 4-hydroxyproline).
  • the lefthand direction is the amino terminal direction and the righthand direction is the carboxy-terminal direction, in accordance with standard usage and convention.
  • the lefthand end of single-stranded polynucleotide sequences is the 5′ end the lefthand direction of double-stranded polynucleotide sequences is referred to as the 5′ direction.
  • the direction of 5′ to 3′ addition of nascent RNA transcripts is referred to as the transcription direction sequence regions on the DNA strand having the same sequence as the RNA and which are 5′ to the 5′ end of the RNA transcript are referred to as “upstream sequences”, sequence regions on the DNA strand having the same sequence as the RNA and which are 3′ to the 3′ end of the RNA transcript are referred to as “downstream sequences”.
  • Silent or conservative amino acid substitutions refer to the interchangeability of residues having similar side chains.
  • a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine.
  • Preferred conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine valine, glutamic-aspartic, and asparagine-glutamine.
  • Silent or conservative replacements are those that take place within a family of amino acids that are related in their side chains. Genetically encoded amino acids are generally divided into families: (1) acidic amino acids are aspartate, glutamate; (2) basic amino acids are lysine, arginine, histidine; (3) non-polar amino acids are alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan, and (4) uncharged polar amino acids are glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine.
  • the hydrophilic amino acids include arginine, asparagine, aspartate, glutamine, glutamate, histidine, lysine, serine, and threonine.
  • the hydrophobic amino acids include alanine, cysteine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, tyrosine and valine.
  • families of amino acids include (i) serine and threonine, which are the aliphatic-hydroxy family; (ii) asparagine and glutamine, which are the amide containing family; (iii) alanine, valine, leucine and isoleucine, which are the aliphatic family; and (iv) phenylalanine, tryptophan, and tyrosine, which are the aromatic family.
  • Structural and functional domains can be identified by comparison of the nucleotide and/or amino acid sequence data to public or proprietary sequence databases.
  • computerized comparison methods are used to identify sequence motifs or predicted protein conformation domains that occur in other proteins of known structure and/or function. Methods to identify protein sequences that fold into a known three-dimensional structure are known. Bowie et al. Science 253:164 (1991).
  • sequence motifs and structural conformations that may be used to define structural and functional domains in accordance with the disclosure.
  • a silent or conservative amino acid substitution should not substantially change the structural characteristics of the parent sequence (e.g., a replacement amino acid should not tend to break a helix that occurs in the parent sequence, or disrupt other types of secondary structure that characterizes the parent sequence).
  • Examples of art-recognized polypeptide secondary and tertiary structures are described in Proteins, Structures and Molecular Principles (Creighton, Ed., W. H. Freeman and Company, New York (1984)); Introduction to Protein Structure (C. Branden and J. Tooze, eds., Garland Publishing, New York, N.Y. (1991)); and Thornton et al. Nature 354:105 (1991).
  • the anti-CD19 ⁇ anti-CD47 bispecific antibody 44 which is based on the ⁇ -body technology, is composed by a common heavy chain and two different light chains. These chains are encoded by the plasmid construct 44 (Table 1). When this expression plasmid is transfected in mammalian cells, three molecules are produced by random assembly of the three chains: a monospecific IgG ⁇ (containing two identical ⁇ light chains), a monospecific IgG ⁇ (containing two identical ⁇ light chains), and a bispecific IgG ⁇ (containing one ⁇ light chain and one ⁇ light chain). If the two light chains are expressed at the same rate and assemble equally, the theoretical ratio for the three molecules should be 25% IgG ⁇ , 25% IgG ⁇ and 50% IgG ⁇ .
  • Codon optimization has been performed with the GeneOptimizer® software (GeneArt), on heavy, kappa and lambda chains. Different candidates were generated by cloning the optimized or not chains in the wild type plasmid of encoding the bispecific antibody 44.
  • the common heavy chain and two light chains (one kappa and one lambda) wild-type, optimized or deoptimized codon were cloned into a single mammalian expression pNOVI vector under three independent CMV promoters.
  • the IgG productivity for each construct was evaluated in Peak cells by two independent transient transfections using Lipofectamine 2000. Seven days after transfection, the total IgG expression was assessed by Octet technology. Except for the candidate 15, no major difference between the candidates in term of total IgG productivity was observed. A trend to a decrease in productivity was observed with construct 15 in which all chains had been optimized ( FIG. 2 ). After 10 days of production in PEAK cells, total IgG were purified on Fc XL resin.
  • a gradient of mobile phase A (0.001 M phosphate buffer+1 M ammonium sulphate, pH 3.5) from 85 to 35% and a growing gradient of mobile phase B (0.001 M phosphate buffer+acetonitrile 10%, pH 3.5) from 15% to 100% were applied.
  • a blank was performed with mobile phase A, pH 7.
  • the analysis of HIC area peak shows a trend with increment of the percentage of bispecific for deoptimized candidates 3, 13 and 19 compared to wild-type 44 and optimized 15 and 17.
  • the ratio of monospecific kappa and lambda for 3, 13 and 19 was significantly different compared to 44.
  • Table 2 summarizes the data obtained for candidates expressed in PEAK cells. For the candidates 3, 13 and 19, the final percentage of bispecific obtained was higher, with an increase of the bispecific ratio from 21.6% for 44 to 42.9% for candidate 13. Interestingly, the highest codon deoptimization (construct 19) level of lambda chain increases the productivity of bispecific antibody.
  • candidates 3 and 13 should show an increase in BsAb expression, as the two light chains are expressed at more equivalent levels
  • the ratio of the different forms of IgG was assessed by HIC for all IgG producing pools ( FIG. 7 ).
  • the data shows that the level of monospecific lambda decreases gradually with the deoptimization level and the inverse pattern is observed for monospecific kappa.
  • the bispecific levels reach a maximum of approximately 40% with a very homogenous distribution for the constructs 3 and 13.
  • the unbalanced expression of one of the two chains leads to a reduced level of bispecific production.
  • each candidate was scaled up and supernatants were harvested after 10 days and clarified by centrifugation at 1,300 g for 10 min.
  • the purification process was composed of three affinity steps. First, the CaptureSelect IgG-CHl affinity matrix (Life Technologies) was washed with PBS and then added to the clarified supernatant. After incubation overnight at 4° C., supernatants were centrifuged at 1,000 g for 10 min, the supernatant was discarded and the resin washed twice with PBS. Then, the resin was transferred to spin columns and a solution containing 50 mM glycine at pH 2.7 was used for elution.

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